Sun Oct 9 21:48:18 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 21:48:18 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3214 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 421 has a net charge of -0.6000 !!! WARNING: GLM 555 has a net charge of -0.6000 !!! WARNING: HIZ 559 has a net charge of 0.2000 !!! WARNING: ZN7 775 has a net charge of 1.4000 !!! WARNING: ZN7 779 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6237953 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 45.78500 98.84100 ymin,ymax (A): 2.947000 60.01700 zmin,zma (A): 14.97300 67.53900 x,y,z range (A): 53.05600 57.07000 52.56600 scale (grids/A): 0.6237953 object centre (A): 72.31300 31.48200 41.25600 number of atom coordinates read : 3214 total number of charged atoms : 3069 net assigned charge : 6.425011 assigned positive charge : 491.9627 centred at (gu) : 90.42451 87.83746 90.52141 assigned negative charge : -485.5391 centred at (gu) : 90.32767 87.79873 90.54856 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8408 nv = 96 ne = 84 npr = 62460 no. pairs analyzed = 62460 no. exposed pairs = 4260 no. arc points = 30668 no. surface atoms = 1421 nbur = 1793 mkacc time = 0.2100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 463 mr = 4377 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.4800000 number of dielectric boundary points 4467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3006 ## 289 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 10332 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4516677E-09 3.6952728E-09 midg,1,midg; midg,igrid,midg 3.4238425E-09 5.9227014E-09 1,midg,midg; igrid,midg,midg -2.8802252E-09 1.6104989E-08 gauss-seidel spectral radius is 0.9867531 estimated iterations to convergence 71 setup time was (sec) 0.7800000 now iterating at: 21:48:19 rms-change max change #iterations 0.1461037 24.26224 at 10iterations 1.3639213E-02 1.899109 at 20iterations 1.2780412E-03 0.1723568 at 30iterations 1.2149635E-04 1.7542839E-02 at 40iterations 1.2561811E-05 1.8005371E-03 at 50iterations finished qdiffx linear iterations at : 21:48:23 total time elapsed so far: 4.620000 # loops : 50 mean,max change (kT/e) : 1.2561811E-05 1.8005371E-03 energy calculations done at 4.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.860000 DelPhi exited at 21:48:23 4.863u 0.386s 0:05.55 94.4% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 21:48:23 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3214 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 421 has a net charge of -0.6000 !!! WARNING: GLM 555 has a net charge of -0.6000 !!! WARNING: HIZ 559 has a net charge of 0.2000 !!! WARNING: ZN7 775 has a net charge of 1.4000 !!! WARNING: ZN7 779 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.871386 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 45.78500 98.84100 ymin,ymax (A): 2.947000 60.01700 zmin,zma (A): 14.97300 67.53900 x,y,z range (A): 53.05600 57.07000 52.56600 scale (grids/A): 1.871386 object centre (A): 72.31300 31.48200 41.25600 number of atom coordinates read : 3214 total number of charged atoms : 3069 net assigned charge : 6.425011 assigned positive charge : 491.9627 centred at (gu) : 91.27258 83.51170 91.56336 assigned negative charge : -485.5391 centred at (gu) : 90.98244 83.39583 91.64533 start vw surface at 0.1800000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 91365 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30668 grid for indexing accessible points = 1.400000 m= 31653 mr = 61559 m= 4792 mr = 22297 m= 287 mr = 2676 m= 3 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 1986 time to turn everything in is 0.9100000 number of dielectric boundary points 41483 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 214 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 24047 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6237953 object centre at (A) : 72.31300 31.48200 41.25600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0999997E-03 -1.2176496E-02 midg,1,midg; midg,igrid,midg 9.9450983E-02 3.3777237E-02 1,midg,midg; igrid,midg,midg -2.3768395E-02 1.8343421E-02 gauss-seidel spectral radius is 0.9986624 estimated iterations to convergence 217 setup time was (sec) 1.260000 now iterating at: 21:48:25 rms-change max change #iterations 4.686474 195.6956 at 10iterations 2.204041 75.58530 at 20iterations 1.033159 31.83658 at 30iterations 0.4865078 15.03541 at 40iterations 0.2291121 6.970785 at 50iterations 0.1080488 3.099918 at 60iterations 5.0807621E-02 1.416776 at 70iterations 2.3986647E-02 0.7589102 at 80iterations 1.1276387E-02 0.3392735 at 90iterations 5.3315195E-03 0.1550890 at 100iterations 2.5167486E-03 7.8757688E-02 at 110iterations 1.1909773E-03 3.3998489E-02 at 120iterations finished qdiffx linear iterations at : 21:48:35 total time elapsed so far: 11.20000 # loops : 120 mean,max change (kT/e) : 1.1909773E-03 3.3998489E-02 energy calculations done at 11.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.43000 DelPhi exited at 21:48:35 11.434u 0.463s 0:12.14 97.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 21:48:35 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3214 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 421 has a net charge of -0.6000 !!! WARNING: GLM 555 has a net charge of -0.6000 !!! WARNING: HIZ 559 has a net charge of 0.2000 !!! WARNING: ZN7 775 has a net charge of 1.4000 !!! WARNING: ZN7 779 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.807079 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 45.78500 98.84100 ymin,ymax (A): 2.947000 60.01700 zmin,zma (A): 14.97300 67.53900 x,y,z range (A): 53.05600 57.07000 52.56600 scale (grids/A): 2.807079 object centre (A): 72.31300 31.48200 41.25600 number of atom coordinates read : 3214 total number of charged atoms : 3069 net assigned charge : 6.425011 assigned positive charge : 491.9627 centred at (gu) : 91.90870 80.26730 92.34499 assigned negative charge : -485.5391 centred at (gu) : 91.47350 80.09366 92.46801 start vw surface at 0.1800000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 211424 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30668 grid for indexing accessible points = 1.400000 m= 103495 mr = 150008 m= 35721 mr = 82499 m= 8414 mr = 27431 m= 1191 mr = 5891 m= 76 mr = 725 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 1.500000 no. cavity mid-points inaccessible to solvent = 6971 time to turn everything in is 2.470000 number of dielectric boundary points 93737 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 2.630000 number of grid points assigned charge 24551 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.871386 object centre at (A) : 72.31300 31.48200 41.25600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2710879E-02 -0.2847517 midg,1,midg; midg,igrid,midg 1.351491 0.4105580 1,midg,midg; igrid,midg,midg -0.3051179 0.1978501 gauss-seidel spectral radius is 0.9992903 estimated iterations to convergence 296 setup time was (sec) 2.860000 now iterating at: 21:48:39 rms-change max change #iterations 11.24519 288.2834 at 10iterations 6.771566 141.2740 at 20iterations 4.045609 92.36055 at 30iterations 2.395645 49.73248 at 40iterations 1.414144 30.40701 at 50iterations 0.8335363 15.55286 at 60iterations 0.4892398 9.177594 at 70iterations 0.2874135 5.067322 at 80iterations 0.1683073 2.957542 at 90iterations 9.8393045E-02 1.742085 at 100iterations 5.7477731E-02 0.9822559 at 110iterations 3.3552852E-02 0.5518913 at 120iterations 1.9550297E-02 0.3722391 at 130iterations 1.1417309E-02 0.1974039 at 140iterations 6.6528842E-03 0.1116867 at 150iterations 3.8908701E-03 6.8094254E-02 at 160iterations 2.2650731E-03 3.8027763E-02 at 170iterations 1.3203034E-03 2.1409035E-02 at 180iterations finished qdiffx linear iterations at : 21:48:59 total time elapsed so far: 23.17000 # loops : 180 mean,max change (kT/e) : 1.3203034E-03 2.1409035E-02 energy calculations done at 23.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.38000 DelPhi exited at 21:49:00 23.387u 0.486s 0:24.14 98.8% 0+0k 0+0io 0pf+0w